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On 22/03/2012 5:13 AM, francesco oteri wrote:
<blockquote
cite="mid:CAFQcp-N0ZLi_Do7skw-DrUDbgmEgF+WUzvVqbp+GcF6JjyX=eA@mail.gmail.com"
type="cite">
<div>
<div>
<div>Hi Mark,</div>
<div>these are the involved residues extracted by the .top
(CSA and CSB are cysteines with modified partial charges):</div>
<div><br>
</div>
<div>; residue 62 CSB rtp CSB q -0.5</div>
<div> 1010 NH1 62 CSB N 1010 -0.47
14.007 ; qtot 0.53</div>
<div> 1011 H 62 CSB HN 1011 0.31
1.008 ; qtot 0.84</div>
<div> 1012 CT1 62 CSB CA 1012 0.07
12.011 ; qtot 0.91</div>
<div> 1013 HB 62 CSB HA 1013 0.09
1.008 ; qtot 1</div>
<div> 1014 CT2 62 CSB CB 1014 -0.05
12.011 ; qtot 0.95</div>
<div> 1015 HA 62 CSB HB1 1015 0.051
1.008 ; qtot 1.001</div>
<div> 1016 HA 62 CSB HB2 1016 0.051
1.008 ; qtot 1.052</div>
<div> 1017 S 62 CSB SG 1017 -0.57
32.06 ; qtot 0.482</div>
<div> 1018 C 62 CSB C 1018 0.51
12.011 ; qtot 0.992</div>
<div> 1019 O 62 CSB O 1019 -0.51
15.999 ; qtot 0.482</div>
<div>; residue 65 CSA rtp CSA q -0.3</div>
<div> 1043 NH1 65 CSA N 1043 -0.47
14.007 ; qtot 0.012</div>
<div> 1044 H 65 CSA HN 1044 0.31
1.008 ; qtot 0.322</div>
<div> 1045 CT1 65 CSA CA 1045 0.07
12.011 ; qtot 0.392</div>
<div> 1046 HB 65 CSA HA 1046 0.09
1.008 ; qtot 0.482</div>
<div> 1047 CT2 65 CSA CB 1047 -0.03
12.011 ; qtot 0.452</div>
<div> 1048 HA 65 CSA HB1 1048 0.08
1.008 ; qtot 0.532</div>
<div> 1049 HA 65 CSA HB2 1049 0.08
1.008 ; qtot 0.612</div>
<div> 1050 S 65 CSA SG 1050 -0.39
32.06 ; qtot 0.222</div>
<div> 1051 C 65 CSA C 1051 0.51
12.011 ; qtot 0.732</div>
<div> 1052 O 65 CSA O 1052 -0.51
15.999 ; qtot 0.222</div>
<div>; residue 112 ASN rtp ASN q 0.0</div>
<div> 1006 NH1 112 ASN N 1006 -0.47
14.007 ; qtot -4.732</div>
<div> 1007 H 112 ASN HN 1007 0.31
1.008 ; qtot -4.422</div>
<div> 1008 CT1 112 ASN CA 1008 0.07
12.011 ; qtot -4.352</div>
<div> 1009 HB 112 ASN HA 1009 0.09
1.008 ; qtot -4.262</div>
<div> 1010 CT2 112 ASN CB 1010 -0.18
12.011 ; qtot -4.442</div>
<div> 1011 HA 112 ASN HB1 1011 0.09
1.008 ; qtot -4.352</div>
<div> 1012 HA 112 ASN HB2 1012 0.09
1.008 ; qtot -4.262</div>
<div> 1013 CC 112 ASN CG 1013 0.55
12.011 ; qtot -3.712</div>
<div> 1014 O 112 ASN OD1 1014 -0.55
15.999 ; qtot -4.262</div>
<div> 1015 NH2 112 ASN ND2 1015 -0.62
14.007 ; qtot -4.882</div>
<div> 1016 H 112 ASN HD21 1016 0.32
1.008 ; qtot -4.562</div>
<div> 1017 H 112 ASN HD22 1017 0.3
1.008 ; qtot -4.262</div>
<div> 1018 C 112 ASN C 1018 0.51
12.011 ; qtot -3.752</div>
<div> 1019 O 112 ASN O 1019 -0.51
15.999 ; qtot -4.262</div>
<div>; residue 114 ILE rtp ILE q 0.0</div>
<div> 1041 NH1 114 ILE N 1041 -0.47
14.007 ; qtot -4.732</div>
<div> 1042 H 114 ILE HN 1042 0.31
1.008 ; qtot -4.422</div>
<div> 1043 CT1 114 ILE CA 1043 0.07
12.011 ; qtot -4.352</div>
<div> 1044 HB 114 ILE HA 1044 0.09
1.008 ; qtot -4.262</div>
<div> 1045 CT1 114 ILE CB 1045 -0.09
12.011 ; qtot -4.352</div>
<div> 1046 HA 114 ILE HB 1046 0.09
1.008 ; qtot -4.262</div>
<div> 1047 CT3 114 ILE CG2 1047 -0.27
12.011 ; qtot -4.532</div>
<div> 1048 HA 114 ILE HG21 1048 0.09
1.008 ; qtot -4.442</div>
<div> 1049 HA 114 ILE HG22 1049 0.09
1.008 ; qtot -4.352</div>
<div> 1050 HA 114 ILE HG23 1050 0.09
1.008 ; qtot -4.262</div>
<div> 1051 CT2 114 ILE CG1 1051 -0.18
12.011 ; qtot -4.442</div>
<div> 1052 HA 114 ILE HG11 1052 0.09
1.008 ; qtot -4.352</div>
<div> 1053 HA 114 ILE HG12 1053 0.09
1.008 ; qtot -4.262</div>
<div> 1054 CT3 114 ILE CD 1054 -0.27
12.011 ; qtot -4.532</div>
<div> 1055 HA 114 ILE HD1 1055 0.09
1.008 ; qtot -4.442</div>
<div> 1056 HA 114 ILE HD2 1056 0.09
1.008 ; qtot -4.352</div>
<div> 1057 HA 114 ILE HD3 1057 0.09
1.008 ; qtot -4.262</div>
<div> 1058 C 114 ILE C 1058 0.51
12.011 ; qtot -3.752</div>
<div> 1059 O 114 ILE O 1059 -0.51
15.999 ; qtot -4.262</div>
<div>; residue 607 CSB rtp CSB q -0.5</div>
<div> 9693 NH1 607 CSB N 9693 -0.47
14.007 ; qtot -3.248</div>
<div> 9694 H 607 CSB HN 9694 0.31
1.008 ; qtot -2.938</div>
<div> 9695 CT1 607 CSB CA 9695 0.07
12.011 ; qtot -2.868</div>
<div> 9696 HB 607 CSB HA 9696 0.09
1.008 ; qtot -2.778</div>
<div> 9697 CT2 607 CSB CB 9697 -0.05
12.011 ; qtot -2.828</div>
<div> 9698 HA 607 CSB HB1 9698 0.051
1.008 ; qtot -2.777</div>
<div> 9699 HA 607 CSB HB2 9699 0.051
1.008 ; qtot -2.726</div>
<div> 9700 S 607 CSB SG 9700 -0.57
32.06 ; qtot -3.296</div>
<div> 9701 C 607 CSB C 9701 0.51
12.011 ; qtot -2.786</div>
<div> 9702 O 607 CSB O 9702 -0.51
15.999 ; qtot -3.296</div>
<div>; residue 610 CSA rtp CSA q -0.3</div>
<div> 9732 NH1 610 CSA N 9732 -0.47
14.007 ; qtot -3.766</div>
<div> 9733 H 610 CSA HN 9733 0.31
1.008 ; qtot -3.456</div>
<div> 9734 CT1 610 CSA CA 9734 0.07
12.011 ; qtot -3.386</div>
<div> 9735 HB 610 CSA HA 9735 0.09
1.008 ; qtot -3.296</div>
<div> 9736 CT2 610 CSA CB 9736 -0.03
12.011 ; qtot -3.326</div>
<div> 9737 HA 610 CSA HB1 9737 0.08
1.008 ; qtot -3.246</div>
<div> 9738 HA 610 CSA HB2 9738 0.08
1.008 ; qtot -3.166</div>
<div> 9739 S 610 CSA SG 9739 -0.39
32.06 ; qtot -3.556</div>
<div> 9740 C 610 CSA C 9740 0.51
12.011 ; qtot -3.046</div>
<div> 9741 O 610 CSA O 9741 -0.51
15.999 ; qtot -3.556</div>
<div>; residue 615 NI rtp NI q +0.4</div>
<div> 9786 NI 615 NI NI 9786 0.4
58.6934 ; qtot -3.926</div>
<div>; residue 616 CN rtp CN q -0.5</div>
<div> 9787 C 616 CN C1 9787 0.11
12.011 ; qtot -3.816</div>
<div> 9788 N 616 CN N1 9788 -0.61
14.007 ; qtot -4.426</div>
<div>; residue 617 CN rtp CN q -0.5</div>
<div> 9789 C 617 CN C1 9789 0.11
12.011 ; qtot -4.316</div>
<div> 9790 N 617 CN N1 9790 -0.61
14.007 ; qtot -4.926</div>
<div>; residue 618 CO rtp CO q -0.1</div>
<div> 9791 C 618 CO C1 9791 0.22
12.011 ; qtot -4.706</div>
<div> 9792 O 618 CO O1 9792 -0.294
15.999 ; qtot -5</div>
<div><br>
</div>
<div><br>
</div>
<div>While this are the bonds I am referring:</div>
<div><br>
</div>
<div> 1017 9786 1 </div>
<div> 1050 9786 1 </div>
<div> 9700 9786 1 </div>
<div> 9739 9786 1 </div>
<div> 1012 9786 1 *</div>
<div> 1015 9786 1 *</div>
<div> 1016 9786 1 *</div>
<div> 1045 9786 1 *</div>
<div> 1048 9786 1 *</div>
<div> 1049 9786 1 *</div>
<div> 9695 9786 1 *</div>
<div> 9698 9786 1 *</div>
<div> 9699 9786 1 *</div>
<div> 9734 9786 1 *</div>
<div> 9737 9786 1 *</div>
<div> 9738 9786 1 *</div>
<div> 9786 9787 1 </div>
<div> 9786 9789 1 </div>
<div> 9786 9791 1 </div>
</div>
<div><br>
</div>
<div>The bonds with the * are what I call fake. i.e the
couple 1012 9786 involves a bond between the nickel atom and
an hydrogen. </div>
<div>This couple, as well as the other fake couples, disappears
in the .tpr file an interestingly pdb2gmx doesn't signal them.</div>
</div>
</blockquote>
<br>
Your atom numbering is non-unique, so this may be confusing
something. Try pdb2gmx -renumber, and/or feeding the renumbered .gro
file into a second run of pdb2gmx. Also, providing your specbond.dat
would help when seeking answers about how it works...<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAFQcp-N0ZLi_Do7skw-DrUDbgmEgF+WUzvVqbp+GcF6JjyX=eA@mail.gmail.com"
type="cite">
<div>
<div><br>
</div>
<div><br>
</div>
<div>If the phenomena is not yet known, I can give you the data
I used to generate the .top and .tpr.</div>
<div><br>
</div>
<div>Francesco</div>
<div><br>
<div class="gmail_quote">Il giorno 21 marzo 2012 16:18, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
ha scritto:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div class="im"> On 22/03/2012 1:46 AM, francesco oteri
wrote:
<blockquote type="cite">Dear gromacs user,
<div>I noted a strange behavior in topology
generation workflow.</div>
<div><br>
</div>
<div>I have a protein whose active site contains a
Ni atom linked to 4 Cys.</div>
<div>I inserted the 4 bonds by specbonds.dat. When
I run pdb2gmx, I have inspected</div>
<div>the Linking messages and they fit with the
expected topology, I mean pdb2gmx </div>
<div>correctly detects the four bonds
nickel-sulphur. </div>
<div>So I run grompp and the topol.tpr has been
correctly generated.</div>
<div><br>
</div>
<div>Then I compared topol.top and topol.tpr bonds
and I noticed that in topol.top there a lot </div>
<div>of fake-bonds, i.e Ni-hydrogen, Ni-Carbonium. <br>
</div>
</blockquote>
<br>
</div>
Can you show an example of what you interpret as a fake
bond?<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span>
<div class="im"><br>
<br>
<blockquote type="cite">
<div><br>
</div>
<div>I dumped topol.tpr through gmxdump, and I
noticed that these bonds are no more present</div>
<div>and only "right" bonds are present.</div>
<div><br>
</div>
<div>So, I am wondering why the fake bonds are
inserted in topol.top and how grompp detectes</div>
<div>these bonds.</div>
<div><br>
</div>
<div><br>
</div>
<div>Francesco</div>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div>
</div>
<br>
--<br>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Cordiali saluti, Dr.Oteri Francesco<br>
</div>
</div>
<br>
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</blockquote>
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